Perform Positional Analogue Scanning using the SMILES Manager Extension

In this tutorial, you will learn how to run a simple but powerful technique, called positional analogue scanning, in order to generate new analogs of your molecules directly in SAMSON using the SMILES Manager extension. This new functionality was inspired by this blog post from Pat Walters and this paper from Lewis Pennington, Ingo Muegge, and coworkers. It will allow you to evaluate the effects of newly introduced changes of your molecules on their properties, like the binding affinity (using Autodock Vina Extended SAMSON…

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Computing normal modes that open a binding site

In this tutorial, we will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Extension. This SAMSON Extension computes the nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134). First, you have to import a structure. For this tutorial I used the 1vpk PDB entry. Then, you launch the NMAL module and indicate the desired number of modes,…

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Using the SMILES Manager

In this tutorial, you will learn how to use the SMILES Manager extension of SAMSON. This extension is based on RDKit. As some of you know, RDKit is an open-source toolkit for cheminformatics which is widely used. One of its features is the conversion of molecules SMILES strings to a 2D and 3D structures. The module interface presents two tabulations: Manage SMILES and Replace fragments. We will present these two sections one by one as they are totally independent. In…

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Calculating non-linear normal modes

In this tutorial, we will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Extension. This SAMSON Extension is an advanced version of the Normal Modes Analysis SAMSON Extension also available on SAMSON Connect. This SAMSON Extension computes nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134). First, you have to import a structure. For this…

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Computing non-linear normal modes of biomolecules

Hello all, Welcome to this tutorial. Here, I will present you the functionalities of the Normal Modes Analysis Lite (NMAL) SAMSON Element. This SAMSON Element computes the nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134, DOI: 10.1021 / acs.jctc.7b00197.). First, you have to import a structure. For this tutorial I used the 1vpk PDB entry. Then, you launch the…

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